What OS are you running?
The Linux kernel now defaults to completely fair queing which might be great for a desktop but is often stupid for a server. This can be altered at boot time and possibly if you build your own kernel.
We dumped Linux for FreeBSD 7.0 with the new ULE scheduler running a stand alone version of MySQL.
We also made MySQL run -10 in "nice"
The application is Vicidial so even though "MySQL claims 30% better performance running on the same server as the application, that was not viable as Asterisk does not play well with others.

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"The future is here. It's just not evenly distributed.